rs7090117

Variant names:

• chr10-123889949-T-C
• rs7090117
• NM_198148.3:c.304+1407A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198148.3(CPXM2):​c.304+1407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,024 control chromosomes in the GnomAD database, including 1,466 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1466 hom., cov: 32)
• Consequence: CPXM2 NM_198148.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 1 publications found

Genes affected

CPXM2 (HGNC:26977): (carboxypeptidase X, M14 family member 2) Predicted to enable metallocarboxypeptidase activity. Predicted to be involved in peptide metabolic process and protein processing. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPXM2	NM_198148.3	c.304+1407A>G		intron_variant	Intron 1 of 13	ENST00000241305.4	NP_937791.2
CPXM2	XM_005269528.4	c.304+1407A>G		intron_variant	Intron 1 of 13		XP_005269585.1
CPXM2	XM_011539283.3	c.304+1407A>G		intron_variant	Intron 1 of 13		XP_011537585.1
CPXM2	XM_017015673.2	c.-23-9640A>G		intron_variant	Intron 2 of 14		XP_016871162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPXM2	ENST00000241305.4	c.304+1407A>G		intron_variant	Intron 1 of 13	1	NM_198148.3	ENSP00000241305.3
CPXM2	ENST00000615851.4	c.-1209+1407A>G		intron_variant	Intron 1 of 14	5		ENSP00000483180.1
CPXM2	ENST00000368854.7	n.175-9640A>G		intron_variant	Intron 2 of 19	2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19679 AN: 151908 Hom.: 1467 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0922

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.117

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.130 AC: 19688 AN: 152024 Hom.: 1466 Cov.: 32 AF XY: 0.129 AC XY: 9599 AN XY: 74292

African (AFR) AF: 0.200 AC: 8284 AN: 41424

American (AMR) AF: 0.0920 AC: 1405 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 446 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5174

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4814

European-Finnish (FIN) AF: 0.123 AC: 1297 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7592 AN: 67988

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.122 Hom.: 320

Bravo AF: 0.132

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.47
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7090117; hg19: chr10-125649465;